ArcGIS for Server connections in ArcMap or ArcCatalog cannot be made with Security Assertation Markup Language (SAML) enterprise accounts if the server is federated with Portal for ArcGIS, which utilizes enterprise logins.
The Portal for ArcGIS Web Adaptor URL must be added to the Portal for ArcGIS connections within ArcGIS Administrator (Advanced->Manage Portal Connections). When making the publisher or administrator connection within ArcCatalog or ArcMap, supply the ArcGIS for Server URL, but leave the username and password field blank, select Finish and a Window pop-up with the option to sign in using the (Security Assertation Markup Language) SAML account.